Human pluripotent stem cell-based system for generating endothelial cells

ABSTRACT

The present invention relates to chemically defined and xenogeneic material-free methods for deriving endothelial cells from human pluripotent stem cells. In particular, the present invention provides highly efficient and reproducible methods of obtaining human endothelial cells from human pluripotent stem cells, where endothelial cells derived from the methods provided herein are suitable for clinically relevant therapeutic applications.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application claims the benefit of U.S. Application Ser. No.62/098,838, filed Dec. 31, 2014, which is incorporated herein as if setforth in its entirety.

STATEMENT REGARDING FEDERALLY FUNDED RESEARCH OR DEVELOPMENT

This invention was made with government support under TR000506 awardedby the National Institutes of Health. The government has certain rightsin the invention.

BACKGROUND

Pluripotent stem cells offer a potentially powerful tool for improvingin vitro models and investigating the underlying mechanisms of humanblood vessel formation, but many challenges remain in generating humanpluripotent-derived endothelial cells (ECs) suitable for large-scaleuse. For example, standard protocols for generating and expanding ECpopulations use animal-derived reagents that are often poorly defined,pose safety concerns for use in clinical applications, and contribute tohighly variable results and limited reproducibility. The majority ofstudies have been performed in rodent models, leaving much to be desiredfor the study of the human cell type. There remains a need in the art,therefore, for efficient, reproducible, and xenogeneic material-freemethods for differentiating human pluripotent stem cells intoendothelial cells suitable for clinical cell therapies and forpredictive analysis of candidate toxic agents.

SUMMARY OF THE INVENTION

In a first aspect, provided herein is a method of isolating humanendothelial cells. The method comprises culturing human pluripotent stemcells to obtain a cell population comprising at least 50% CD31⁺endothelial cells. Culturing comprises, in order: (i) culturing thepluripotent stem cells for about two days in a chemically definedculture medium comprising a serum-free growth supplement, a BoneMorphogenetic Protein (BMP), and Activin A; and (ii) culturing thecultured cells of (i) for about three days in a chemically definedculture medium that comprises a serum-free growth supplement and doesnot comprise Transforming Growth Factor Beta 1 (TGFβ1), whereby thecultured cells differentiate into endothelial cells. The culture mediumof (ii) can comprise one or more factors selected from the groupconsisting of VEGF, BMP4, BMP2, BMP7, and an inhibitor of TGFβ1-mediatedsignaling. The inhibitor of TGFβ1-mediated signaling can be selectedfrom the group consisting of SB431542 and A-83-01. The cell populationcan comprise at least 75% CD31⁺ endothelial cells. The cell populationcan comprise at least 50% CD31⁺/CD34⁺ endothelial cells. In some cases,the chemically defined culture medium of (i) further comprises a ROCKinhibitor. The ROCK inhibitor can be selected from the group consistingof Y27632 and Blebbistatin. The human pluripotent stem cells can becultured in the presence of vitronectin. The vitronectin can berecombinant human vitronectin.

In another aspect, this document provides an isolated cell population ofCD31+ endothelial cells obtained according to a method described herein.

In a further aspect, this document provides a method of testing acompound. The method comprises exposing the compound to a population ofCD31⁺ endothelial cells obtained according to a method described hereinand examining the effect of the compound on endothelial cell growth ordevelopment.

These and other features, objects, and advantages of the presentinvention will become better understood from the description thatfollows. In the description, reference is made to the accompanyingdrawings, which form a part hereof and in which there is shown by way ofillustration, not limitation, embodiments of the invention. Thedescription of preferred embodiments is not intended to limit theinvention to cover all modifications, equivalents and alternatives.Reference should therefore be made to the claims recited herein forinterpreting the scope of the invention.

INCORPORATION BY REFERENCE

All publications, patents, and patent applications mentioned in thisspecification are herein incorporated by reference to the same extent asif each individual publication, patent, and patent application wasspecifically and individually indicated to be incorporated by reference.

This application includes a sequence listing in computer readable form(a “txt” file) that is submitted herewith. This sequence listing isincorporated by reference herein.

BRIEF DESCRIPTION OF THE DRAWINGS

This patent or application file contains at least one drawing executedin color. Copies of this patent or patent application publication withcolor drawing(s) will be provided by the Office upon request and paymentof the necessary fee.

FIGS. 1A-1G demonstrate the generation and characterization of human ES-and iPS-cell derived endothelial cells. (A) Schematic of endothelialcell differentiation protocol. (B) Flow cytometric analysis of CD31 andCD34 expression at days 0 (pluripotent state) and 5 (differentiatedstate). (C) Flow cytometric analysis of KDR, NANOG and OCT4 expressionat days 0 and 5. (D) RNA-seq analysis of H1 human ES cells, pericytes,HUVEC, CD31⁺CD34⁻, and CD31⁺CD34⁺ cells. Heat map of relativetranscription levels was shown. Human ES cell enriched gene expression(TPM) was normalized to H1 human ES cells. Vascular gene expression wasnormalized to CD31⁺CD34⁻ cell. (E) In vitro Matrigel® encapsulationassay of ECs. (F) In vivo Matrigel® plug angiogenesis of CD31⁺CD34⁻cells. (G) H9 human ES and four iPS cell lines were subjected toendothelial differentiation. Cells were analyzed by flow cytometry atday 5. Scale Bar: 100 μm.

FIGS. 2A-2P demonstrate further optimization of multiple components toengineer capillary beds in synthetic PEG gels. (A-C) ECs were culturedin PEG gel (45% cross-linking with 2 mM RGD), with or withoutfibronectin or pericyte. CD31⁺ECs (green) and SM22α⁺ pericytes (purple)are labeled. “-” indicates ECs; “+FN” indicates ECs+fibronectin. In(E-G), different concentrations of RGD were used. EC-pericytes wereco-cultured in 45% cross-linked hydrogels with fibronectin. In (I-K),gel stiffness was varied. EC-pericytes were co-cultured in 2 mM RGDhydrogels with fibronectin. 35%/45%/60% of the norbornene group wascross-linked by MMP-sensitive peptide to modulate gel stiffness. (D, H,L) The vascular area density (the ratio of vascular covered area tototal area) was measured by Nikon NIS element. Data represent mean±SD(n>=3), *:p<0.05. In (M-O), EC-pericytes were co-cultured in 2 mM RGD,50% cross-linked hydrogels with fibronectin at different time point.(M′-O′) Higher magnification of M-P. Scale Bar: 100 μm. Note: Hydrogelsof (A-I) were formed at the bottom of 24-well plate while hydrogels of(M-P) were formed in a transwell insert to improve nutrient diffusion.(P) Clustering analysis of RNA-seq data (TPM) was generated byclustering algorithm of Galaxy (Distance of matrix: Pearson correlation,type of linkage: average).

FIGS. 3A-3F present data demonstrating that the ERK pathway modulates ECresponse to 3D microenvironment. (A) Western blot showed ERK activity in2D and 3D culture. (B) Western blot showed U0126 decreased ERK activity.(C) Click-it EdU assay showed U0126 treatment decreased ECproliferation. (D) Top 10 (TPM>100, top 10 fold change) vasculature(TPM>100, Top 10 fold change) (AmiGO, GO:0001944) and cell cycle genes(AmiGO, GO:0007049) from RNA-seq. Full gene list of vasculature and cellcycle was generated by Amigo. (E) RT-qPCR revealed that inhibition ofERK pathway increased vasculature gene expression but suppressed cellcycle gene expression. Data was normalized to DMSO control (not shown).(F) RT-qPCR demonstrated that knockdown ERK2 by SiRNA enhancedvasculature gene expression and suppressed cell cycle gene expression.Data was normalized to NT control. ERK2i, siRNA of ERK2. NT,non-targeting.

FIGS. 4A-4C are images of marker expression in endothelial cells. (A, B)Immunostaining was performed to characterize CD31 and CD144 expressionof purified endothelial cells. (C) LDL uptake assay. Scale Bar: 100 μm.Anti-CD31-PE (BD PharMingen, clone WM-59), Anti-CD34-APC (BD PharMingen,clone 581), Anti-CD31 (Dako, cat #M0823), Anti-VE-cadherin (BDPharmingen, cat #555661), Anti-SM22a (Abcam, cat #ab14106), acetylatedlow-density lipoprotein (LDL-FITC, Invitrogen).

FIGS. 5A-5D presents FAK pathway data. (A) Western blot showed FAKactivity in 2D and 3D culture. (B) Western blot showed inhibition of FAKactivity by 20 μM Inhibitor-14 (1-14″) treatment. (C) 1-14 suppressedcell proliferation. (D) RT-qPCR revealed 1-14 treatment decreased bothvasculature and cell cycle gene expression.

FIG. 6 depicts endothelial cell survival upon U0126 treatment intwo-dimensional (2D) culture.

FIG. 7 demonstrates improved endothelial cell purity followingpassaging. P0: the human pluripotent stem cells underwent endothelialcell differentiation for five days. P1: the differentiated endothelialcells were passaged and cultured in E7V media for another two to threedays.

DETAILED DESCRIPTION OF THE INVENTION

Since animal-derived albumins like bovine serum albumin are xenogeneic(i.e., derived from, originating in, or being a member of a non-humanspecies) and are known to exhibit substantial lot-to-lot variability,standard protocols for obtaining endothelial cells that require BSAyield cells that are not compatible with clinical applications for humansubjects and not sufficiently uniform for in vitro applications such asdrug screening and modeling human development or disease. The presentinvention is based at least in part on the Inventors' discovery ofBSA-free, xenogeneic material-free (“xeno-free”) protocols fordifferentiating human pluripotent stem cells into endothelial cellsunder chemically defined conditions. In particular, populations of CD31⁺endothelial cells (ECs) were generated from both human embryonic stemcells (human ES cells) and induced pluripotent stem cells (human iPScells) using xeno-free, chemically-defined protocols. Based on thesediscoveries, the present invention provides fully defined and xeno-freemethods of producing and expanding clinically relevant human endothelialcells for clinical cell therapies and tissue modelling applications. Inparticular, the present invention provides a fully defined and xeno-freemethod of producing and expanding clinically relevant human endothelialcells for clinical cell therapies and tissue modelling applications.Accordingly, the compositions and methods described herein also providea unique opportunity to study these cells in a three-dimensional humantissue construct.

In a first aspect, therefore, the present invention provides a method ofgenerating endothelial cells. The method comprises differentiating humanpluripotent stem cells under xenogen-free, chemically defined (i.e., inthe presence of a chemically defined medium) conditions that promotedifferentiation to endothelial cells. In exemplary embodiments,differentiating comprises culturing human pluripotent stem cells in achemically defined culture medium comprising a serum-free growthsupplement and one or more endothelial cell differentiating factors,whereby a cell population comprising human CD31⁺ endothelial cells isobtained.

According to methods of the present invention, human pluripotent cellsare cultured in a chemically defined culture medium comprising aserum-free growth supplement. As used herein, the terms “chemicallydefined medium” and “chemically defined culture medium” are usedinterchangeably and refer to formulations of biochemically-definedconstituents that can include constituents of known chemicalcomposition. As used herein, the terms “chemically defined medium” and“chemically defined cultured medium” also refer to a culture mediumcontaining formulations of fully disclosed or identifiable ingredients,the precise quantities of which are known or identifiable and can becontrolled individually. As such, a culture medium is not chemicallydefined if (1) the chemical and structural identity of all mediumingredients is not known, (2) the medium contains unknown quantities ofany ingredients, or (3) both. Standardizing culture conditions by usinga chemically defined culture medium minimizes the potential forlot-to-lot or batch-to-batch variations in materials to which the cellsare exposed during cell culture. Accordingly, the effects of variousdifferentiation factors are more predictable when added to cells andtissues cultured under chemically defined conditions. As used herein,the term “serum-free” refers to cell culture materials that are free ofserum obtained from animal (e.g., fetal bovine) blood. Culturing cellsor tissues in the absence of animal-derived materials (i.e., underxenogen-free conditions) reduces or eliminates the potential for suchcross-species viral or prion transmission. As used herein, the terms“xenogen-free” and “xeno-free” are used interchangeably and refer tocell or tissue culture conditions that avoid the use of xenogeneicmaterials including, without limitation, animal-derived cells, exudates,or other constituents of animal (e.g., non-human) origin. As usedherein, the term “xeno-free” also refers to a medium free of any cell orcell product of a species other than that of the cultured cell. Humanproteins are preferred but not essential for chemically definedconditions, provided that uncharacterized animal products are excluded.

In exemplary embodiments, a method of the present invention providescomprises differentiating human pluripotent stem cells underxenogen-free, chemically defined conditions (i.e., in the presence of achemically defined medium), whereby the pluripotent stem cellsdifferentiate into cells having an early mesoderm phenotype. As usedherein, “an early mesoderm phenotype” includes expression of brachyury,which is considered to be one of the best markers of mesoderm cells andis used to track the development of the mesodermal lineage. Brachyury isexpressed transiently in all cells ingressing through the primitivestreak as well as in the nascent and early migrating mesoderm. Wilkinsonet al., Nature 343:657-9 (1990); Herrmann et al., Development 113:913-7(1991). Other markers of an early mesoderm phenotype include, withoutlimitation, FoxF1, GATA4, Isl1, Tbx20, PDGFR-alpha, and PDGFR-beta. Asused herein, “mesodermal cells” refers to reference to mesodermal-likecells or cells which are committed to differentiate into mesodermalcells. Reference herein to “mesodermal cells” includes any cell ofmesodermal lineage such as mesendoderm, extraembryonic mesoderm andembryonic mesoderm, as well as their partially or terminallydifferentiated progenitors.

Preferably, human pluripotent stem cells are cultured in achemically-defined basal culture medium formulation comprising thedefined components of culture medium “DF3 S” as set forth in Chen etal., Nature Methods 8:424-429 (2011), which is incorporated by referenceherein as if set forth in its entirety. As used herein, the terms “E7culture medium” and “E7” are used interchangeably and refer to achemically defined culture medium comprising or consisting essentiallyof DF3S supplemented to further comprise insulin (20 μg/mL), transferrin(10.67 ng/mL) and human Fibroblast Growth Factor 2 (FGF2) (100 ng/mL).As used herein, the terms “E8 culture medium” and “E8” are usedinterchangeably and refer to a chemically defined culture mediumcomprising or consisting essentially of DF3S supplemented by theaddition of insulin (20 μg/mL), transferrin (10.67 ng/mL), human FGF2(100 ng/mL), and human TGFβ1 (Transforming Growth Factor Beta 1) (1.75ng/mL).

In exemplary embodiments, human pluripotent stem cells are cultured forabout two days in the presence of a serum-free, chemically-definedculture medium that is supplemented to further comprise bonemorphogenetic protein 4 (BMP4) and Activin-A. As used herein, the term“E8BA medium” refers to an E8 medium supplemented to comprise BMP4 andActivin A. In some cases, the chemically defined culture medium furthercomprises a Rho kinase (ROCK) inhibitor selected from the groupconsisting of Y-27632, Blebbistatin (a selective and high-affinity smallmolecule inhibitor of myosin heavy chain ATPase), and HA1077 (fasudil).

In some cases, the method further comprises culturing the cells in aserum-free, chemically defined culture medium that does not compriseTGFβ1. For example, cells can be further cultured in the presence of achemically-defined culture medium comprising or consisting essentiallyof the following defined components: DMEM-F12, NaHCO₃, L-Ascorbic Acid,selenium, transferrin, insulin, and FGF2. In exemplary embodiments,human pluripotent stem cells are cultured in the presence of an E7defined medium supplemented to further comprise VEGFA (“E7V medium”) orto comprise VEGFA, a bone morphogenetic protein (e.g., BMP4, BMP2, orBMP7), and an inhibitor of TGFβ1-mediated signaling (e.g., SB431542,A-83-01) (“E7BVi medium” or “E7BVi”).

In some cases, a method of the invention comprises culturing humanpluripotent stem cells in a medium comprising or consisting essentiallyof the following defined components: DMEM/F12, L-ascorbicacid-2-phosphate magnesium (64 mg/l), sodium selenium (14 μg/l), FGF2(100 μg/l), insulin (20 mg/l), NaHCO₃ (543 mg/l), transferrin (10.7mg/l), TGFβ1 (2 μg/l) BMP-4 (5 μg/l), and Activin-A (25 μg/l). In othercases, the method further comprises culturing the pluripotent stem cellsin a medium comprising or consisting essentially of the followingdefined components: DMEM/F12, L-ascorbic acid-2-phosphate magnesium (64mg/l), sodium selenium (14 μg/l), FGF2 (100 μg/l), insulin (20 mg/l),NaHCO₃ (543 mg/l), transferrin (10.7 mg/l), and VEGFA (50 μg/l).

In yet other cases, a method of the invention comprises culturing humanpluripotent stem cells in a medium comprising or consisting essentiallyof the following defined components: DMEM/F12, L-ascorbicacid-2-phosphate magnesium (64 mg/l), sodium selenium (14 μg/l), FGF2(100 μg/l), insulin (20 mg/l), NaHCO₃ (543 mg/l), transferrin (10.7mg/l), VEGFA (50 μg/l), BMP4 (50 μg/l), and SB431542 (5 μM). In somecases, BMP2 or BMP7 is used in place of BMP4. In some cases, theinhibitor of TGFβ1-mediated signaling A-83-01 is used in place ofSB431542.

CD31 is an antigenic marker for mature endothelial cells lining thelumen of blood vessels (Tepper et al., Blood 105:1068-1077 (2005)) andserves as an early indicator of endothelial differentiation(Kanayasu-Toyoda et al., J. Biol. Chem. 282:33507-14 (2007)).Endothelial progenitor cells mature into CD31⁺ endothelial cells.Accordingly, endothelial cells obtained according to a method of thepresent invention have one of the following expression profiles:CD31⁺/CD34⁺ and CD31⁺/CD34⁻. Human CD31⁺/CD34⁺ cells have been shown toform networks of capillary-like structures when seeded on Matrigel (Wanget al., Nature Biotechnology 24(3):317-8 (2007)). Cell populationsobtained by a method of the present invention comprise at least 30%(e.g., at least 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95%, or more)CD31-positive (“CD31⁺”) cells. Following an additional 3 days inculture, CD31⁺/CD34⁻ endothelial cells differentiate into CD31⁺CD34⁺cells. Endothelial cells derived from ES cells differ from circulatingEPCs in that human ES cell-derived ECs secrete significantly higherlevels of cytokines VEGF and Ang-1 as compared to EPCs obtained fromhuman cord blood, and also demonstrate significantly acceleratedre-epithelialization and wound healing in a wound model as compared tocirculating EPCs (Park et al., Biomaterials 34:995-1003 (2013)).

As used herein, “pluripotent stem cells” appropriate for use accordingto a method of the invention are cells having the capacity todifferentiate into cells of all three germ layers. Suitable pluripotentcells for use herein include human ES cells and human inducedpluripotent stem cells (iPS cells). As used herein, “embryonic stemcells” or “ES cells” mean a pluripotent cell or population ofpluripotent cells derived from an inner cell mass of a blastocyst. SeeThomson et al., Science 282:1145-1147 (1998). These cells express atleast Oct-4, SSEA-3, SSEA-4, TRA-1-60, or TRA-1-81, and appear ascompact colonies having a high nucleus to cytoplasm ratio and prominentnucleolus. ES cells are commercially available from sources such asWiCell Research Institute (Madison, Wis.). As used herein, “inducedpluripotent stem cells” or “iPS cells” mean a pluripotent cell orpopulation of pluripotent cells that may vary with respect to theirdifferentiated somatic cell of origin, that may vary with respect to aspecific set of potency-determining factors and that may vary withrespect to culture conditions used to isolate them, but nonetheless aresubstantially genetically identical to their respective differentiatedsomatic cell of origin and display characteristics similar to higherpotency cells, such as ES cells, as described herein. See, e.g., Yu etal., Science 318:1917-1920 (2007).

iPS cells exhibit morphological properties (e.g., round shape, largenucleoli and scant cytoplasm) and growth properties (e.g., doubling timeof about seventeen to eighteen hours) akin to ES cells. In addition, iPScells express pluripotent cell-specific markers (e.g., Oct-4, SSEA-3,SSEA-4, Tra-1-60 or Tra-1-81, but not SSEA-1). iPS cells, however, arenot immediately derived from embryos. As used herein, “not immediatelyderived from embryos” means that the starting cell type for producingiPS cells is a non-pluripotent cell, such as a multipotent cell orterminally differentiated cell, such as somatic cells obtained from apost-natal individual.

In another aspect, the present invention provides methods for obtainingxenogen-free endothelial cells derived from a particular mammaliansubject (e.g., a particular human subject). For example, it may beadvantageous to obtain endothelial cells that exhibit one or morespecific phenotypes associated with or resulting from a particulardisease or disorder of the particular mammalian subject. In some cases,subject-specific cells for use in a neural construct of the inventionare induced pluripotent stem cells obtained by reprogramming somaticcells of an individual human subject according to methods known in theart. See, for example, Yu et al., Science 324(5928):797-801 (2009); Chenet al., Nat Methods 8(5):424-9 (2011); Ebert et al., Nature457(7227):277-80 (2009); Howden et al., Proc Natl Acad Sci USA108(16):6537-42 (2011). Human induced pluripotent stem cell-derivedendothelial cells allow modeling of drug responses in tissue constructsthat recapitulate neural or other tissue in an individual having, forexample, a particular disease. Even the safest drugs may cause adversereactions in certain individuals with a specific genetic background orenvironmental history. Accordingly, iPS cell-derived endothelial cellsobtained according to methods of the present invention from individualshaving known susceptibilities or resistances to various drugs ordiseases will be useful in identifying genetic factors and epigeneticinfluences that contribute to variable drug responses.

Subject-specific somatic cells for reprogramming into inducedpluripotent stem cells can be obtained or isolated from a target tissueof interest by biopsy or other tissue sampling methods. In some cases,subject-specific cells are manipulated in vitro prior to use in a neuralconstruct of the invention. For example, subject-specific cells can beexpanded, differentiated, genetically modified, contacted topolypeptides, nucleic acids, or other factors, cryo-preserved, orotherwise modified prior to use in a neural construct of the presentinvention.

In some cases, endothelial cell populations obtained according to amethod of the present invention are combined with other cell types toobtain various endothelial cell-derived or endothelial cell-associatedcells and tissues. For example, endothelial cells obtained according toa method of the present invention can be provided with vascular smoothmuscle cells to promote blood vessel formation in a three-dimensionalhydrogel-based tissue construct as described in Attorney Docket Nos.960296.01937.P140400US02 and 960296.01935.P140410US02, filedconcurrently as U.S. application Ser. No. ______, and U.S. applicationSer. No. ______, respectively (serial numbers to be provided), which areincorporated herein as if set forth in their entirety. Endothelial cellsand mesenchymal cells contribute to an interconnected vasculature withinthe tissue construct. Isolated endothelial cells and endothelial cellpopulations generated from hPSCs according to the methods providedherein will be beneficial for many potential applications such asengineering new blood vessels, endothelial cell transplantation into theheart for myocardial regeneration, induction of angiogenesis fortreatment of regional ischemia, and screening for drugs affectingvasculature such as angiogenesis inhibition to slow cancer progression.

In exemplary embodiments, human pluripotent stem cells (e.g., human EScells or iPS cells) are cultured in the absence of a feeder layer (e.g.,a fibroblast layer) and in the presence of a chemically defined,xenogen-free substrate. For example, human pluripotent cells can becultured in the presence of a substrate comprising vitronectin, avitronectin fragment or variant, a vitronectin peptide, a self-coatingsubstrate such as Synthemax® (Corning), or combinations thereof. Inexemplary embodiments, the chemically-defined, xeno-free substrate is aplate coated in recombinant human vitronectin peptides or polypeptides(e.g., recombinant human vitronectin).

The expression of a number of cell type-associated markers (or the lackthereof) can be used to characterize endothelial cells obtainedaccording to the methods provided herein. For example, the expression ofsome markers associated with pluripotency in hPSCs decline over thecourse of differentiation of the hPSCs into the endothelial lineage.Such pluripotency markers include Oct4, Nanog, SSEA-3, SSEA-4, TRA-1-60,and TRA-1-81.

Suitable methods for detecting the presence or absence of biologicalmarkers are well known in the art and include, without limitation,immunohistochemistry, qRT-PCR, RNA sequencing, and the like forevaluating gene expression at the RNA level. For example, a cellpopulation obtained according to a method provided herein can beevaluated for expression of biological markers of endothelial cells.RT-PCR is useful to verify the expression of known endothelial cell (EC)markers including CD31 (PECAM), CD34, CD144 (VE-cadherin), and VonWillebrand factor (vWF). In some cases, endothelial phenotypes of suchcells can be evaluated using immunofluorescence staining for a varietyof EC surface antigens such as, without limitation, human CD34, CD31,and KDR (VEGF receptor). Quantitative methods for evaluating expressionof markers at the protein level in cell populations are also known inthe art. For example, flow cytometry is used to determine the fractionof cells in a given cell population that express or do not expressbiological markers of interest (e.g., CD31, CD34).

As described in the Examples section below, differentiation of humanpluripotent stem cells into ECs according to methods of the presentinvention can be confirmed based on expression of endothelial cellmarkers (e.g., CD31, CD34, CD144/CDH5/VE-cadherin). Endothelial cellidentity is also associated with upregulation of KDR/VEGFR2 geneexpression, upregulation of vasculogenesis and angiogenesis markers, anddownregulation of pluripotency markers such as NANOG and OCT4 (relativeto human ES cells or induced pluripotent stem cells). Silencing ofpluripotency markers was observed in both CD31+CD34- and CD31+CD34+ cellpopulations compared to H1 ES cells.

Unless defined otherwise, all technical and scientific terms used hereinhave the same meaning as commonly understood by one of ordinary skill inthe art to which the invention belongs. Although any methods andmaterials similar to or equivalent to those described herein can be usedin the practice or testing of the present invention, the preferredmethods and materials are described herein.

As used herein, “a medium consisting essentially of” means a medium thatcontains the specified ingredients and those that do not materiallyaffect its basic characteristics.

As used herein, “serum-free” means that a medium does not contain serumor serum replacement, or that it contains essentially no serum or serumreplacement. Likewise, an “albumin free” culture medium means a mediumthat does not contain albumin or is essentially free of albumin. As usedherein, “effective amount” means an amount of an agent sufficient toevoke a specified cellular effect according to the present invention.

As used herein, the term “about” means within 5% of a statedconcentration range, density, temperature, or time frame.

The invention will be more fully understood upon consideration of thefollowing non-limiting Examples. It is specifically contemplated thatthe methods disclosed are suited for pluripotent stem cells generally.All papers and patents disclosed herein are hereby incorporated byreference as if set forth in their entirety.

EXAMPLES Example 1—Endothelial Cell Differentiation Under Xeno-FreeConditions

Materials and Methods

Reagents: Anti-CD31-PE (BD PharMingen, clone WM-59), Anti-CD34-APC (BDPharMingen, clone 581), Anti-CD31 (Dako, cat #M0823), Anti-VE-cadherin(BD Pharmingen, cat #555661), Anti-SM22a (Abcam, cat #ab14106),acetylated low-density lipoprotein (LDL-FITC, Invitrogen). Batch 1 BSA(Fisher Scientific, cat #BP1606, lot 106563), Batch 2 BSA (Sigma, cat#A7906, lot 069K1653), batch 3 BSA (Sigma, cat #A9647, lot 071M1487V),Batch 4 BSA (Miltenyi Biotec, cat #130-091-376, lot 5120309144), Batch 5BSA (Sigma, cat #2153, lot 066K0738), Batch 6 BSA (Sigma, cat #A9418),and Batch 7 BSA (Sigma, cat #A9576, lot SLBB5246). Note: themanufacturer labels Batch 6 and 7 BSA with “suitable for cell culture,”but Batch 5 (and not Batches 6 and 7) supported cell survival during ECdifferentiation.

Human ES/iPS Cell Culture: All human ES/iPS cells were maintained in E8medium on Matrigel®-coated tissue culture plates, and were passagedroutinely with EDTA as described previously (Chen et al., Nature Methods8(5):424-9 (2011)). Cell line 005B23.1 was derived from skin punchfibroblast and maintained on recombinant human vitronectin-coatedplates. Cell line DF19.11 was derived from foreskin fibroblast. Cellline CD-3-1 was derived from cord blood cell. PBMCs were peripheralblood mononuclear cells.

Endothelial cell differentiation, purification, and culture: 80-90%confluence ES/iPS cells were dissociated by TrypLE (Invitrogen) for 3minutes at 37° C. Cells were plated on vitronectin-coated plate(comprising recombinant vitronectin, 60 μg/plate) at 1:3 ratios (1 to1.5×10⁵ cells/cm²). 10 μM Y27632 (ROCK inhibitor) was used on the firstday to improve cell survival. Cells were cultured in E8BA or E8BAC (E8BAsupplemented with 1 μM CHIR99021) (used in FIG. 2) for two days and thenswitched to E7BVi or other medium (used in FIG. 2) for another threedays. To isolate CD31⁺CD34⁺ cells, cells were labeled with CD34 magneticbeads and processed through autoMACS (Miltenyi Biotec). To isolateCD31⁺CD34⁻ cells, the side population from above was further labeledwith CD31 beads and purified by autoMACS. Purified CD31⁺CD34⁻ cells werecultured on fibronectin-coated plate with E7V medium.

Depending on the cell line, cell populations comprising 50%-90%endothelial cells were achieved by day 5. Endothelial celldifferentiation can be induced by E7Vi, E7Bi, E7, or E6V medium. E7Bimedium mainly induced CD31⁺CD34⁻ cells, while E7V and E7Vi mainlyinduced CD31⁺/CD34⁺ cell differentiation.

TABLE 1 Chemically Defined Cell Medium Components Medium ChemicallyDefined Components E8 DMEM/F12; L-ascorbic acid-2-phosphate magnesium(64 mg/l); sodium selenium (14 μg/1); human FGF2 (100 μg/l); insulin (20mg/l); NaHCO₃ (543 mg/l); transferrin (10.7 mg/1); TGFβ1 (2 μg/l) E8BAE8 medium + 5 μg/l BMP4 and 25 μg/l Activin A E7 DMEM/F12; L-ascorbicacid-2- phosphate magnesium (64 mg/1); sodium selenium (14 μg/l); humanFGF2 (100 μg/l); insulin (20 mg/l); NaHCO₃ (543 mg/l); and transferrin(10.7 mg/l) E7BVi E7 medium + 50 μg/l VEGF + 50 μg/l BMP4 + 5 μMSB431542 E7Bi E7 medium + 50 μg/l BMP4 + 5 μM SB431542 E7Vi E7 medium +50 μg/l VEGF + 5 μM SB431542 E6 DMEM/F12; L-ascorbic acid-2-phosphatemagnesium (64 mg/l); sodium selenium (14 μg/l); insulin (20 mg/l);NaHCO₃ (543 mg/l); and transferrin (10.7 mg/l) E6V E6 medium + 50 μg/lVEGF

3D Matrigel® encapsulation assay: 1.5×10⁶ endothelial cells/ml and0.75×10⁶ pericytes/ml (ScienCell, cat #1200) were encapsulated in 5mg/ml Matrigel®. A 10 μL monomer/cell solution was spotted in the middleof 24-well plate and incubated for 5 minutes at 37° C. forsolidification. E7V medium was then applied. Immunostaining wasperformed on day 4 and the structures were imaged using confocalmicroscopy.

In vivo Matrigel® plug angiogenesis assay: 5×10⁵ endothelial cells wereresuspended in 100 μl E7V medium and 200 μL Matrigel. A 300 μL cellMatrigel mixture was subcutaneously injected into the neck of nude mice.After inoculation for two weeks, the injected plug was harvested, fixed,and immunostained.

RNA-sequencing and data processing: Total RNA was isolated by RNeasy Kit(Qiagen). A cDNA library was prepared by Illumina TruSeq protocol andsequenced by HiSeq 2500. Data processing was performed as previouslydescribed. See Stewart et al., PLoS Comput. Biol. 9:e1002936 (2013).Briefly, FASTQ files of nucleotide sequence were generated byCASAVA(v1.8.2) and reads were mapped to human transcriptome (hg19,v1.1.17) with Bowtie(v0.12.8) (Langmead et al., Genome Biol. 10:R25(2009)). The gene expression was calculated by RSEM (RNA-seq byExpectation-Maximization) (v1.1.21).

Results and Discussion

Previous protocols for deriving ECs have been difficult to reproduce andoften require biological components derived from animal sources that arepoorly defined. Descamps et al., Vascul. Pharmacol. 56:267-279 (2012).Therefore, we derived endothelial cells using defined conditions,including recombinant vitronectin for surface coating, xeno-freedifferentiation medium, and no bovine serum albumin (BSA). Using ourBSA-free and xeno-free protocol, we explored the influence of materialson human vasculogenesis by using synthetic hydrogels with adaptablebiochemical and mechanical properties.

We developed a defined 3D model for blood vessel formation in whichhuman pluripotent stem cell-derived endothelial cells (ECs) are culturedwithin synthetic extracellular matrices (sECM). ECs (50%-80% CD31⁺cells; six separate cell lines) were derived from both embryonic stemcells (ESCs) and induced pluripotent stem cells (iPSCs) using ourxeno-free, chemically-defined protocol: human pluripotent stem cellswere first differentiated into cells having mesoderm identity using BMP4and Activin-A (E8BA medium) for two days. These mesoderm cells were thentreated with BMP4, VEGFA, and SB431542 (a TGF-β receptor inhibitor)(E7BVi medium) for another three days, yielding both CD31⁺CD34⁻ andCD31⁺CD34⁺ EC populations (FIGS. 1a-b ). EC fate was further confirmedby upregulation of KDR/VEGFR2 and downregulation of NANOG and OCT4 (FIG.1c ). Silencing of other ESC enriched genes was observed in bothCD31⁺CD34⁻ and CD31⁺CD34⁺ cell populations compared to H1 ESCs (FIG. 1d). Vasculogenesis/angiogenesis genes for both EC populations wereupregulated (FIG. 1d ). Furthermore, ECs expressed endothelial markersCD144 (CDH5/VE-cadherin), internalized LDL (FIG. 4), and formedcapillary networks in vitro and in vivo (FIGS. 1e-f ). Importantly, ourprotocol generated 50-80% CD31⁺ endothelial cells from two ESC (H1 andH9) and four iPSC (DF19.11, CD-3-1, PBMC-3-1, and 005B-23.1) sources(FIG. 1g ), including an iPSC (005B-23.1) line that was establishedusing chemically defined xeno-free conditions. Therefore, these datademonstrate robust and efficient generation of human ECs in chemicallydefined conditions, thus addressing a crucial production requirement forpotential clinical applications.

We first investigated roles for individual components of the 3Dmicroenvironment during vascular network formation, including soluble(fibronectin, FN), insoluble (CRGDS), mechanical (matrix crosslinkingdensity), and cellular (pericytes) factors. Limited cellularorganization was observed for ECs cultured in media without FN (FIG. 2a), while the addition of soluble FN induced vascular network formation(FIG. 2b ). Interconnected vascular networks were pronounced when ECswere cocultured with pericytes in sECM, leading to a quantitativeincrease in vascular area density (FIGS. 2d-h ). Matrix propertiesplayed an important role in vascular organization in sECM, as networkformation was minimal in the absence of RGD, while the highest vascularcoverage was observed for intermediate RGD concentrations (FIGS. 2e-h ,constant 45% crosslinking) and matrix crosslinking density (FIG. 2i-l );constant 2 mM RGD). Finally, vascular networks persisted for at least 16days when cultured using our optimized conditions (FIGS. 2m-p ). Thus,vascular network formation was optimal when ECs were cocultured withpericytes in sECM and could be tuned by changing cell adhesion liganddensity or matrix mechanical properties of the synthetic scaffold.

We performed RNA-sequencing (RNA-seq) to compare global gene expressionof cells cultured in sECM versus standard 2D and 3D platforms usingtwo-dimensional clustering and Spearman's pairwise rank correlation(FIG. 2p ). Global gene expression was highly correlated for EC-pericytecocultures in sECM vs. Matrigel (Spearman's correlation, p=0.98-0.99),with comparisons at both days 1 and 3 being approximately equivalent toexpected correlation between biological replicates. Individual celltypes were also highly correlated for 3D monocultures in sECM atdifferent time points (ρ˜0.97-0.98; days 1 vs 3), but were lesscorrelated when comparing 2D cultured on TCP and 3D culture in sECM(ρ˜0.95) (FIG. 2p , further discussed below). Together, our resultsdemonstrate that a defined sECM provides the necessary cues to modelglobal 3D vascular function similarly to Matrigel; the gold standardmaterial for vasculogenesis¹⁶.

We further investigated 3D vascular network formation by EBseq³¹analysis (FDR≤0.005) to analyze differential gene expression. Weidentified cell type-specific mechanisms that mediated 3D vascularnetwork formation in sECM by identifying characteristic gene expressionprofiles for ECs and pericytes in 3D culture. We gained further insightinto functional characteristics for ECs and pericytes in 3D culture byusing DAVID Gene Ontology (GO) Functional Classification ³²(GOTERM_BP_FAT algorithm) to identify functional gene signatures. ECsand pericytes distinctly expressed a wide range of genes associated withblood vessel formation^(8,33-36), including vasculature development,cell-matrix adhesion (e.g., integrins), ECM components (e.g., collagenand laminin), and proteases (e.g., MMPs). Characteristic genes includedcell-type specific growth factor-receptor pairs known to be importantfor blood vessel formation and stabilization, such as EC enrichment forKDR (VEGFR2), PDGFA, PDGFB, HBEGF, and CXCR4, and pericyte enrichmentfor the complementary genes VEGFA, PDGFRA, PDGFRB, EGFR (alsoERBB2/EGFR-2), and CXCL12/SDF-1 (GF-Receptor genes) ^(8,33-35). Intotal, we identified 583 genes enriched in ECs (relative to pericytes)and 640 genes enriched in pericytes (relative to ECs) in 3D sECM forboth days 1 and 3.

Further analysis of specific gene sets for ECs and pericytes suggesteddistinct roles for remodeling the ECM during vascular network formation.ECs and pericytes each expressed ECM isoforms associated with basementmembrane assembly including collagen IV and laminin, which are localizedon vascular networks formed within PEG hydrogels²¹. However, our resultssuggested that pericytes played a predominant role for producingcollagens I and III, as COL1A1, COL1A2, and COL3A1 isoforms were eachcharacterized by >25-fold higher expression than ECs at days 1 and 3.Pericytes were also characterized by enhanced expression for genesimplicated in collagen I and III matrix assembly, including >70-foldhigher fibronectin (FN1) expression and >5-fold higher all-integrinexpression, an integrin implicated in remodeling^(37,38), but which tothe best of our knowledge has not been specifically investigated for arole during blood vessel formation. Further, pericytes werecharacterized by enriched α10-integrin and its receptors collagen IV(several isoforms; also expressed by ECs), collagen VI (COL6A1, COL6A2,and COL6A3; pericyte-enriched), and laminin-1 (LAMA1, LAMB1, LAMC1;pericyte-enriched)³⁹. Finally, α9-integrin plays a role duringangiogenesis by binding VEGFA and thrombospondin-1 (THSD1)^(40,41) eachof which was enriched for EC gene expression. Taken together, theseresults demonstrate the value of a fully defined 3D vascular model andglobal gene expression profiling for identifying relationships betweenECs and pericytes.

Engineered materials that mimic the extracellular matrix (ECM) haveplayed an increasing role in deconstructing the 3D microenvironment byproviding strict control over biochemical and biophysical properties²⁸,and several approaches to investigate and promote blood vessel formationhave been reported. ^(4,16-18) To investigate cellular and extracellularinfluences on 3D vascular network formation, we fabricated a syntheticextracellular matrix (sECM) permissive towards cellular remodeling using“thiol-ene” chemistry^(19,24) to crosslink 8-arm poly (ethylene glycol)(PEG) molecules with MMP-degradable peptides²⁹ and to incorporatependant RGD (Arg-Gly-Asp)-containing peptides for cell adhesion³⁰. Wethen compared global gene expression for cells cultured in sECM totissue culture polystyrene (TCP) and Matrigel, which are common 2D and3D in vitro culture formats for investigating vascular biology.

Due to the differences in clustering for 2D compared to 3D monocultures(FIG. 2p ), we further analyzed differential gene expression for ECscultured in sECM (3D culture) or on TCP (2D culture), and identified“GO” functional terms using DAVID^(32,42). Genes related to vascularmorphogenesis and remodeling were upregulated in 3D culture^(8,33-35),including cell adhesion genes (e.g., GO:0007155˜cell adhesion; 49genes), cell migration genes (e.g., GO:0006928˜cell motion; 34 genes),and blood vessel morphogenesis genes (e.g., GO:0001944˜vasculaturedevelopment; 23 genes). In contrast, ECs were primarily characterized byhigher expression of proliferation genes in 2D compared to 3D culture,as 9 out of the top 10 upregulated gene sets were cell cycle-related.These data demonstrate that vascular networks can form in chemicallydefined materials with minimal components and provide insights into howmaterials instruct tissue modeling.

We investigated a potential role for ERK signaling on cell cycle geneexpression for ECs cultured on TCP surfaces since ERK regulates ECfunctions that include proliferation, blood vessel morphogenesis, andmechanotransduction^(34,35,43-46) Phosphorylated ERK1/2 (pERK1/2) washigher for ECs on TCP compared to cells cultured in sECM (FIG. 3A),which demonstrates that ERK activity was increased when using thestandard 2D culture platform. We further investigated the role for ERKactivity in regulating the shift to a proliferative phenotype bycomparing the top 10 enriched cycle genes from 2D culture and vasculardevelopment genes from 3D culture (Day 3) for ECs on TCP after pERKinhibition (FIGS. 3b-d ). ECs on TCP were first treated with the MEKinhibitor U0126 (an upstream regulator of ERK phosphorylation), whichreduced proliferation and decreased the expression of cell cycle genesin a dose-dependent manner (10 of 10 genes downregulated) (FIGS. 3b-c ).The reduction in cell cycle gene expression correlated to increasedexpression of 3D-like vascular development genes for ECs on TCP (8 of 10genes upregulated; FIG. 3e ). Reduced cell cycle and increased vasculardevelopment gene expression was observed when ERK2 was silenced by RNAi(FIG. 3f ), which confirms results using MEK inhibitor to reduce ERKsignaling. These combined results suggest that over-activation of ERKsignaling disrupts the expression of vascular development genes andinduces a proliferative phenotype for ECs cultured on TCP.

Cells cultured on TCP are exposed to a non-physiological planar surfaceand a modulus that is orders of magnitude higher than mosttissues^(47,48), which is notable since matrix mechanical propertiesregulate proliferation through a focal adhesion kinase (FAK)-ERKsignaling loop for 2D and 3D culture^(43,49). Increased pFAK expressionwas observed for ECs on TCP (FIG. 5a ), while the pFAK inhibitor 1-14reduced pERK expression and proliferation (FIGS. 5b-c ). However, FAKinhibition had only limited effect on 3D-like vascular genes (FIG. 5d ),which differs from the influence of ERK inhibition (FIG. 3). Therefore,our results support a role for FAK-ERK signaling in mediating mechanicalcues that regulate proliferation⁴⁹⁻⁵¹, but suggest that the influence ofERK on vascular expression is regulated by FAK-independent signaling.Complete inhibition of ERK activity induced cell death for ECs on TCP(FIG. 6), which is consistent with previous results demonstrating thatblocking ERK induces apoptosis^(44,45) and that ERK is a positiveregulator of vascular function^(43,44). These combined results indicatethat moderate ERK signaling is required for EC survival and vasculargene expression, but that overexpressed ERK (such as on TCP surfaces)induces a shift to a proliferative phenotype that disrupts normalvascular function.

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We claim:
 1. An isolated cell population of human pluripotent stemcell-derived CD31⁺ endothelial cells obtained according to a methodcomprising: culturing human pluripotent stem cells to obtain a cellpopulation comprising at least 50% CD31⁺ endothelial cells, whereinculturing comprises, in order: (i) culturing the pluripotent stem cellsfor about two days in a chemically defined culture medium comprising aserum-free growth supplement, a Bone Morphogenetic Protein (BMP), andActivin A; and (ii) culturing the cultured cells of (i) for about threedays in a chemically defined culture medium that comprises a serum-freegrowth supplement and does not comprise Transforming Growth Factor Beta1 (TGFβ1), whereby the cultured cells differentiate into endothelialcells.